Can you check the original file properties ('mplayer -identify' output would be nice to have) and post them here? It might have something special in it. Also try watching both the original and converted file with the pc version of MPlayer (http://www.mplayerhq.hu/design7/dload.html) and some other video players to check if there are any sync problems.

Audio sync problems could be caused by mplayer not having enough cpu resources to play video in realtime (if you disabled -framedrop option for example). Try transcoding the same video with lower bitrate/resolution and check if it helps.

Another source of problems could be DSP audio decoder, you can try running mplayer with '-ao esd -ac ffmp3' options to use ARM core for decoding audio.

If nothing helps, I'll try to download and have a look at this video file myself.

Even if you find a solution that works for you, please provide some kind of feedback, it may help other people having the same problem. Thanks.